Energy-based advection modelling using bond graphs

Abstract

Advection, the transport of a substance by the flow of a fluid, is a key process in biological systems. The energy-based bond graph approach to modelling chemical transformation within reaction networks is extended to include transport and thus advection. The approach is illustrated using a simple model of advection via circulating flow and by a simple pharmacokinetic model of anaesthetic gas uptake. This extension provides a physically consistent framework for linking advective flows with the fluxes associated with chemical reactions within the context of physiological systems in general and the human physiome in particular.

A review of the diverse applications of bond graphs in biology and physiology

“…Moreover, this method was used to study heterogeneities in the diffusion coefficient along the thickness of the membrane. Recently, the passive transport mechanism inside cells has been modelled using BGs [136] and an equivalent BG concept of advection has been devised by Gawthrop & Pan [137].…”

Energy-based Modelling of Single Actin Filament Polymerisation Using Bond Graphs

“…Bond graphs were introduced by Paynter [13,14] to model energy transduction within and between different physical domains including electrical, mechanical and hydraulic; a number of introductory texts are available [15][16][17]. Bond graph models of chemical reaction networks were introduced in the seminal papers of Oster et al [18,19], and later extended in the context of Systems Biology [20][21][22][23][24][25][26][27]. A recent introduction and overview of the bond graph approach to systems biology is available [28] and and a short introduction to bond graph modelling is given as [22,Appendix A].…”

Sensitivity Analysis of Biochemical Systems Using Bond Graphs

“…A detailed account is given by Oster et al [38] and an overview of the approach is given by Perelson [39]. This work has been extended to Systems Biology [28,[40][41][42][43][44][45][46].…”